iipimage and a performance analysis of jpeg2000 encoding

IIPImage & An Analysis of JPEG2000 Encoding Parameters Ruven Pillay, [email protected]>

IIPImage & IIPImage & An Analysis of JPEG2000 Encoding An Analysis of JPEG2000 Encoding

ParametersParametersRuven Pillay

C2RMF

Wellcome Trust, London, 10th November 2014


1. IIPImage2. Museum Imaging4. Multispectral & Hyperspectral Imaging5. Scientific Applications6. JPEG2000 Encoding Parameters


IIPImage


Imaging Challenge in Museums

Images getting larger and larger. New imaging technologies, new imaging techniques produce massivemassive quantities of data ...


Scientific Imaging in Museums

Scientific imaging techniques can produce quantitative data in 16, 32 bit formats

Xray Infra-red Raking Light UV Emmisography

Images Copyright ©C2RMF 2014Image Credits: Elsa Lambert, Elisabeth Ravaud


Spectral Imaging in Museums

Multi/Hyper spectral imaging can produce gigabytes of data and hundreds of channels per pixel

Multispectral Imaging Hyperspectral Imaging


Image Visualization Software: IIPImage

● Open source● Networked remote viewing● Single source → multiple uses● High resolution images – up to

terrapixel sizes● Region export / resizing● Gamma, contrast adjustments,

rotation etc.● Multi-platform● Images stored in standard

archive formats: TIFF or JPEG2000

http://iipimage.sf.net


Web Services API

● Basic Image Processing Parameters– Contrast: CNT=c– Gamma: GAM=g– Thresholding: MINMAX=c:min,max– Band recombination: CTW=[N:M]– Profile: PFL=r:x1,y1-x2,y2– Spectral reflectance: SPECTRA=r,x,y– Color map: CMP=JET– Inversion: INV


Protocol Support

IIPImage can handle multiple access protocols● IIP (Internet Imaging Protocol)● Zoomify● Deepzoom● IIIF (International Image Interoperability Framework)


Museum Imaging Examples


Extreme Resolutions

Image Copyright ©C2RMF 2014Image Credits: Elsa Lambert, Guy BazileThe Last Supper (1506), Marco D'Oggiono: Xray: 131,022 x 60,669 pixels (7 gigapixels)


Monitoring Change

Im ages du r ing resto ra t ion p rocess

Before Restoration During Restoration After Restoration

Images Copyright ©C2RMF 2014Image Credits: Ruven Pillay, Jean-Louis Bellec

The Virgin and Child with Saint AnneLeonardo da VinciOil on Panel1.68 x 1.30 mMusée du Louvre


Comparing Imaging Modalities

Im ages o f sam e ob ject us ing d iffe ren t cam e ras o r techn iques

The Bedroom at Arles (1889)Vincent van GoghOil on Canvas57.5 x 74.0 cmMusée d'Orsay

Images Copyright ©C2RMF 2014Image Credits: Ruven Pillay, Elsa Lambert, Elisabeth Ravaud


Image Blending

http://merovingio.c2rmf.cnrs.fr/iipimage/iipmooviewer-2.0/vangogh.html Images Copyright ©C2RMF 2014Image Credits: Ruven Pillay

http://merovingio.c2rmf.cnrs.fr/iipimage/iipmooviewer-2.0/vangogh.html


Linking Images and Data

● Make images a gateway through which to explore and understand

● Link additional scientific data directly into image

Portrait of a Woman with a Mirror (1515)TitianOil on Canvas93 x 76 cmMusée du Louvre Image Copyright ©C2RMF 2014

Image Credits: Ruven Pillay


High Resolution Multispectral & Hyperspectral Imaging


Multispectral Imaging

Description independent of environment

– Acquisition of many colour channels (10's)

– Acquisition of reflectance spectrum

– Quantitative measurements


Spectral Reconstruction

Images Copyright ©C2RMF 2014Image Credits: Ruven Pillay


Hyperspectral Imaging at the C2RMF

● Spectral Range– Visible – Near Infrared

(400-1000nm)– Up to 160 bands

● Spatial Resolution– 15 pixels / mm– 65 microns– 385 dpi


Hyperspectral Imaging of Marquetry

● Major study and restoration of Louvre's André-Charles Boulle collection

● Marquetry consisting of multiple types of painted wood

Images Copyright ©C2RMF 2014Image Credits: Thomas Clot


Wardrobe Doors (~1700)André Charles BoulleMarquetry (255.0 x 157.0 cm)Musée du Louvre

Inlaid Marquetry



Technical Imaging

Color UV Fluorescence X-ray

Images Copyright ©C2RMF 2014Image Credits: Thomas Clot, Jean Marsac


Comparing Wavelengths

Wardrobe Doors (~1700)André Charles BoulleMarquetry (255.0 x 157.0 cm)Musée du Louvre

20GB Data Cube● 7nm spectral

sampling● 8241 x 16177 pixels

spatiallyComparison of Color vs narrow spectral bands:● 412nm● 992nm



Who Uses IIPImage

● Cultural heritage institutions:– Museums: National Gallery of Art, Washington,

National Gallery, London, C2RMF / Louvre– Libraries: The European Library, BNF, The National

Library of Wales, University Libraries– UNESCO, Wikimedia Commons, Wellcome Foundation,

Mellon Foundation● Science

– Micro-biology: Virtual nanoscopy applications, biomedical applications

– Astronomy: NASA, Institute of Astrophysics: sky surveys, astrophysics data


Biomedical Applications



● Virtual nanoscopy - Creation of large virtual slides– Regions up to 1 mm2 at nm

resolution– Transmission electron

microscopy– Resulting slide:

● 1,461 × 604 µm2 in size● 921,600 × 380,928 pixels● Each pixel 1.6 nm square● Total of 281 gigapixels

[1] F. G. A. Faas, M. C. Avramut, B. M. van den Berg, A. M. Mommaas, A. J. Koster, and R. B. G. Ravelli, “Virtual nanoscopy: Generation of ultra-large high resolution electron microscopy maps,” J Cell Biol, vol. 198, no. 3, pp. 457–469, Aug. 2012.



[1] Z. Husz, N. Burton, B. Hill, N. Milyaev, and R. Baldock, “Web tools for large-scale 3D biological images and atlases,” BMC Bioinformatics, vol. 13, no. 1, p. 122, Jun. 2012.

● MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, UK

● Woolz 3D data● IIP3D - extension to IIP

protocol for 3D cross-sections

● Atlas of mouse embryo development

● 3D Volumetric Data● Annotations● Anatomy ontology

http://www.emouseatlas.org/


Astrophysics Applications


Astronomy

● Sky Surveys:– VISTA Variables in the Via Lactea

(VVV)– Galactic Plane Survey (GPS)

● VISTA (Visible and Infrared Survey Telescope for Astronomy), Chile– 3 tonne camera– 16 IR detectors– 67 million pixels

● Data:– 100-200 TB of raw data– 3 IR wavelengths combined to

create false color image– Image containing 1 billion stars– 100GB TIFF of entire galactic plane– 1,267,500 x 120,000 pixels

http://djer.roe.ac.uk/vsa/vvv/iipmooviewer-2.0-beta/lb.html

http://djer.roe.ac.uk/vsa/vvv/iipmooviewer-2.0-beta/lb.html


Terabyte Scientific Data

● Calibrated sky survey data– Full 32 bit per

channel floating point data

– 1.3TB TIFF file● Access to line

profiles● Star catalogue

integration

Institute of Astrophysics (IAP)http://visiomatic.iap.fr/demo/large.html

http://visiomatic.iap.fr/demo/large.html


Digital Elevation Maps

Dynamically color-mapped DEM data / hill-shading, Mars: HiRISE Project (NASA/JPL/University of Arizona)


Getting and Installing IIPImage


Build & Package Support

● Debian / Ubuntu– apt-get install iipimage-server

● Fedora / CentOS / RHEL– yum install iipsrv

● Compilation from source– Github:

https://github.com/ruven/iipsrv– Linux, Solaris, Mac OSX, Windows– GCC, Clang, VC++

● Web Server Environments– Apache, Lighttpd, NginX, Stand-

alone


Analysis of JPEG2000 Encoding Parameters


JPEG2000

Encoding parameters can make a big difference to image

– Encoding time– File size– Decoding speed for streaming applications

● Can make large difference to IIPImage performance● JPEG2000 parameter choice a dark art


Parameter Analysis

● Parameters– Tile sizes (0 → 4096x4096)– Precincts (0 → 1024x1024)– Codeblocks (0 → 64x64)– Software (Kakadu & OpenJPEG)– → 864 combinations

● Test image (505MB)– 15016x11741 pixels– 3 channel RGB– 8 bits per channel


Encoding: File Size

TIFF Deflate: 0.566TIFF LZW: 0.624


Encoding: File Size


Encoding: Speed


Decoding Time vs Precinct Size for Various Code Block Sizes


Tile Decoding Time vs JPEG2000 Tile Size Using Ideal Precinct/Code Block Sizes at

Different Resolutions


Access Analytics: Tile Index vs Number of Hits for Demo Image on IIPImage Website


Averaged Tile Decoding Time Across All Resolutions vs JPEG2000 Tile Encoding Sizes

Using Ideal Precinct / Code Block Sizes


http://iipimage.sourceforge.net

http://iipimage.sourceforge.net/



Thank You

Website: http://iipimage.sourceforge.netGithub: https://github.com/ruven/iipsrv

Facebook: http://www.facebook.com/IIPImageTwitter: http://twitter.com/iipimage

Email: [email protected]


iipimage and a performance analysis of jpeg2000 encoding

Documents